Intron sequences

The expression of many of these molecules has been studied during various stages of differentiation of normal neutrophils and also of corresponding leukemic cells employing molecular biology techniques (eg, measurements of their specific mRNAs). For the majority, cDNAs have been isolated and sequenced, amino acid sequences deduced, genes have been localized to specific chromosomal locations, and exons and intron sequences have been defined. Some important proteinases of neutrophils are listed in Table 52-12. 

In searching for regulatory elements it is clear that particular attention must be given to intron sequences. The homeobox gene intron sequences are often well conserved, with the mouse and human Hox-4.4 introns and the mouse and human Hox-1.3 introns being almost identical (Renucci et al., 1992 Toumier-Lasserve et al., 1989). 

Krynetski EY, Fessing MY, Yates CR et al. Promoter and intronic sequences of the human thiopurine S-methyltransfer-ase (TPMT) gene isolated from a human PAC1 genomic library. Pharm Res 1997 14 1672-1678. 

Intron DNA base sequence between exons, the protein-coding parts of a DNA sequence of a gene. Intronic sequences are transcribed into mRNA but they are spliced out of the RNA molecule before translation of RNA into protein (see also exon). 

It contains neither intergenic material away from the coding region nor intronic sequences. 

We have started examining nucleotide compositional strand asymmetries in transcribed regions of human sequences [36]. We have computed the 5ta and 5gc skews [Eq. (1)] for intron sequences since, in contrast to exonic sequences, they can be considered as weakly selected sequences. For each gene, we have concatenated all the introns in a unique sequence (see Section II.A). The distributions of the TA and GC skews, computed on the 14,854 intro-containing... 

A question of interest is the possible existence of correlations between and Sgc skews in intronic sequences without repeats. When all genes are considered, only small correlation is observed (Pearson s correlation coefficient r equals 0.09). However, the values of the skews from small genes turn out to be highly noisy. When one excludes these small genes, 5ta and Sgc present larger correlation (e.g., r = 0.45) for genes with total intron length I > lOkbp and... 

Figure 6. Probability density functions of the skews Sta ( ) and Sac ( ) values computed from the intronic sequences of the 14,854 intron-containing genes after removing repeated sequences, (a) Sense genes (b) antisense genes.

More recently, we have extended this study of strand asymmetries in intron sequences to evolutionarily distant eukaryotes [37]. When appropriately examined, all genomes present transcription-coupled excess of T over A ( TA > 0) in the coding strand. In contrast, GC skew is found positive in... 

Eukaryotic Animal (recombinant) virus vectors Transient or lytic infection Infection in susceptible cells All essential viral genes strong promoter/enhancers polyadenylation signal intron sequences... 

Eukaryotic Mammalian cell-transient expression Transient expression None A higher copy number can be achieved using ori sequence that responds to factors in recipient cells Strong constitutive or inducible promoter polyadenylation signal intron sequences... 

Jenkins, G.J.S.. Mitchell, I. de G. Parry, J.M. (1997) Enhanced restriction site mutation (RSM) analysis of 1,2-dimethylhydrazine induced mutations, using endogenous p53 intron sequences. Mutagenesis, 12, 117-123... 

In most cases, the DNA inserted into the MCS for expression is not a genomic gene with the original exon/intron configuration, but a cDNA. In exceptional cases, antisense RNA or ribozymes may be expressed. cDNA lacks intronic sequences, but still has the 5 and 3 UTR sequences. As discussed above, the presence of the 3 UTR may reduce the stability of mRNA transcribed from the cDNA insert. Furthermore, the length and secondary structure of the 5 UTR may influence the efficiency of translation. Therefore, it is generally recommended to use cDNA with only short 5 and 3 UTR sequences for expression with expression vectors. 

Khamlichi, A.A., Rocca, A. and Cogne, M. (1994) The effect of intron sequences on expression levels of Ig cDNAs. Gene, 150, 387-390. 

Pohjanvirta R, Wong JM, Li W, Harper PA, Tuomisto J, Okey AB. Point mutation in intron sequence causes altered carboxyl-terminal structure in the aryl hydrocarbon receptor of the most 2,3,7,8-tetrachlorodibenzo-p-dioxin-resistant rat strain. Mol Pharmacol 1998 54(l) 86-93. 

The primary RNA transcript from a protein-coding gene in a eukaryotic cell must be modified by several RNA processing reactions in order to become a functional mRNA molecule. The 5 end is modified to form a 5 cap structure. Most pre-mRNAs are then cleaved near the 3 end and a poly(A) tail is added. Intron sequences are removed by RNA splicing. 

RNA splicing The next step in RNA processing is the precise removal of intron sequences... 

Intron sequences contain some common features. Most introns begin with the sequence GT (GU in RNA) and end with the sequence AG. Otherwise, very little similarity exists among them. Intron sequences may be large relative to coding sequences in some genes, over 90 percent of the sequence between the 5 and 3 ends of the mRNA is introns. RNA polymerase transcribes intron sequences. This means that eukaryotic mRNA precursors must be processed to remove introns as well as to add the caps at the 5 end and poly adenylic acid (poly A) sequences at the 3 end. 

The small nuclear ribonucleoprotein particles (snRNPs or snurps ) that carry out the splicing reaction use RNA-RNA basepairing to select the splice sites. Almost all intron-exon junctions contain the sequence AG-GU with the GU beginning the intron sequence. Furthermore, the consensus sequence for the beginning of the intron has a longer sequence complementary to the U1 RNA. Thus, assembly of the splicing complex, called the spliceosome, starts when the RNA component of the U1 snRNP base pairs with the junction between the 3 end of the exon and the 5 end of the intron. See Figure 12-13. 

---